Long-term Variant Scenario Forecasts

• Scenario 1: High Vaccine Efficacy + No Strain - Assumes 25 million courses distributed per month in the future, and efficacy 95% after two doses, 50% after one dose. No new strain more transmissible than existing one(s). Precautions slowly reduced to the most lenient setting since September.
• Scenario 2: High Vaccine Efficacy + New Strain - Assumes 25 million courses distributed per month in the future, and efficacy 95% after two doses, 50% after one dose. New strain 1.5x transmissible than existing one(s). Precautions slowly reduced to the most lenient setting since September.
• Scenario 3: Fatigue+Hesitancy+ No Strain - Assumes current vaccine delivery rates but 50% of population in each category refuse to accept. Efficacy 95% after two doses, 50% after one dose. No new strain more transmissible than existing one(s). Precautions slowly reduced to the most lenient setting since May.
• Scenario 4: Fatigue+Hesitancy+ New Strain - Assumes current vaccine delivery rates but 50% of population in each category refuse to accept. Precautions slowly reduced to the most lenient setting since May. Efficacy 95% after two doses, 50% after one dose. New strain 1.5x transmissible than existing one(s). Precautions slowly reduced to the most lenient setting since May.

% Show variations in cases

[~, sidx] = sort(countries);

ignore_idx = [51, 52, 53, 55, 56];

for ii = 1:length(sidx)

cid = sidx(ii);

if sum(ignore_idx == cid)>0

continue;

end

figure;

x_dat = datetime(2020, 1, 23)+ caldays(2:size(data_4, 2));

p_b = plot(x_dat, diff(data_4(cid, :)), 'r'); hold on;

p_b.Color = 1 - (1-p_b.Color)*0.3;

plot(x_dat, diff(data_4_s(cid, :)), 'r', 'LineWidth', 2); hold on;

xx = diff(squeeze(net_infec_A(:, cid, :))')';

x_dat = datetime(2020, 1, 23)+ caldays(size(data_4, 2)+1:(size(data_4, 2)+size(xx, 2)));

X_plot = [x_dat, fliplr(x_dat)];

Y_plot = [min(xx), fliplr(max(xx))];

plot(x_dat, mean(xx, 1), 'g', 'LineWidth', 2); hold on

fill(X_plot, Y_plot , 1,....

'facecolor','g', ...

'edgecolor','none', ...

'facealpha', 0.3);

hold on

xx = diff(squeeze(net_infec_B(:, cid, :))')';

x_dat = datetime(2020, 1, 23)+ caldays(size(data_4, 2)+1:(size(data_4, 2)+size(xx, 2)));

X_plot = [x_dat, fliplr(x_dat)];

Y_plot = [min(xx), fliplr(max(xx))];

plot(x_dat, mean(xx, 1), 'b', 'LineWidth', 2); hold on

fill(X_plot, Y_plot , 1,....

'facecolor','b', ...

'edgecolor','none', ...

'facealpha', 0.3);

xx = diff(squeeze(net_infec_C(:, cid, :))')';

x_dat = datetime(2020, 1, 23)+ caldays(size(data_4, 2)+1:(size(data_4, 2)+size(xx, 2)));

X_plot = [x_dat, fliplr(x_dat)];

Y_plot = [min(xx), fliplr(max(xx))];

plot(x_dat, mean(xx, 1), 'c', 'LineWidth', 2, 'LineStyle', '--'); hold on

fill(X_plot, Y_plot , 1,....

'facecolor','c', ...

'edgecolor','none', ...

'facealpha', 0.3);

hold on

% xx = diff(squeeze(net_infec_D(:, cid, :))')';

% x_dat = datetime(2020, 1, 23)+ caldays(size(data_4, 2)+1:(size(data_4, 2)+size(xx, 2)));

% X_plot = [x_dat, fliplr(x_dat)];

% Y_plot = [min(xx), fliplr(max(xx))];

% plot(x_dat, mean(xx, 1), 'm', 'LineWidth', 2, 'LineStyle', '--'); hold on

% fill(X_plot, Y_plot , 1,....

% 'facecolor','m', ...

% 'edgecolor','none', ...

% 'facealpha', 0.3);

% Legend entries

h = zeros(4, 1);

h(1) = plot(NaN,'r', 'LineWidth', 2);

h(2) = plot(NaN,'g', 'LineWidth', 2);

h(3) = plot(NaN,'b', 'LineWidth', 2);

h(4) = plot(NaN, 'c', 'LineWidth', 2);

h(5) = plot(NaN, 'm', 'LineWidth', 2, 'LineStyle', ':');

legend(h, 'Observed',...

'Scenario 1: No strain, high vaccine efficacy', 'Scenario 2: High Vaccine Efficacy + Strain', 'Scenario 3: Fatigue/Hesitancy+No Strain', ...

'Scenario 4: Fatigue/Hesitancy+ Strain', 'location', 'northwest');

hold off

xlabel('Date')

ylabel('New Reported Cases');

title(countries{cid});

set(gca, 'FontSize', 18);

set(gcf,'position',[10,10,1200,450]);

% For deaths

figure;

x_dat = datetime(2020, 1, 23)+ caldays(2:size(data_4, 2));

p_b = plot(x_dat, diff(deaths(cid, :)), 'r'); hold on;

p_b.Color = 1 - (1-p_b.Color)*0.3;

plot(x_dat, diff(deaths_s(cid, :)), 'r', 'LineWidth', 2); hold on;

xx = diff(squeeze(net_death_A(:, cid, :))')';

x_dat = datetime(2020, 1, 23)+ caldays(size(data_4, 2)+1:(size(data_4, 2)+size(xx, 2)));

X_plot = [x_dat, fliplr(x_dat)];

Y_plot = [min(xx), fliplr(max(xx))];

plot(x_dat, mean(xx, 1), 'g', 'LineWidth', 2); hold on

fill(X_plot, Y_plot , 1,....

'facecolor','g', ...

'edgecolor','none', ...

'facealpha', 0.3);

hold on

xx = diff(squeeze(net_death_B(:, cid, :))')';

x_dat = datetime(2020, 1, 23)+ caldays(size(data_4, 2)+1:(size(data_4, 2)+size(xx, 2)));

X_plot = [x_dat, fliplr(x_dat)];

Y_plot = [min(xx), fliplr(max(xx))];

plot(x_dat, mean(xx, 1), 'b', 'LineWidth', 2); hold on

fill(X_plot, Y_plot , 1,....

'facecolor','b', ...

'edgecolor','none', ...

'facealpha', 0.3);

xx = diff(squeeze(net_death_C(:, cid, :))')';

x_dat = datetime(2020, 1, 23)+ caldays(size(data_4, 2)+1:(size(data_4, 2)+size(xx, 2)));

X_plot = [x_dat, fliplr(x_dat)];

Y_plot = [min(xx), fliplr(max(xx))];

plot(x_dat, mean(xx, 1), 'c', 'LineWidth', 2, 'LineStyle', '--'); hold on

fill(X_plot, Y_plot , 1,....

'facecolor','c', ...

'edgecolor','none', ...

'facealpha', 0.3);

hold on

% xx = diff(squeeze(net_death_D(:, cid, :))')';

% x_dat = datetime(2020, 1, 23)+ caldays(size(data_4, 2)+1:(size(data_4, 2)+size(xx, 2)));

% X_plot = [x_dat, fliplr(x_dat)];

% Y_plot = [min(xx), fliplr(max(xx))];

% plot(x_dat, mean(xx, 1), 'm', 'LineWidth', 2, 'LineStyle', '--'); hold on

% fill(X_plot, Y_plot , 1,....

% 'facecolor','m', ...

% 'edgecolor','none', ...

% 'facealpha', 0.3);

% Legend entries

h = zeros(4, 1);

h(1) = plot(NaN,'r', 'LineWidth', 2);

h(2) = plot(NaN,'g', 'LineWidth', 2);

h(3) = plot(NaN,'b', 'LineWidth', 2);

h(4) = plot(NaN, 'c', 'LineWidth', 2);

h(5) = plot(NaN, 'm', 'LineWidth', 2, 'LineStyle', ':');

legend(h, 'Observed',...

'Scenario 1: No strain, high vaccine efficacy', 'Scenario 2: High Vaccine Efficacy + Strain', 'Scenario 3: Fatigue/Hesitancy+No Strain', ...

'Scenario 4: Fatigue/Hesitancy+ Strain', 'location', 'northwest');

hold off

xlabel('Date')

ylabel('New Reported Deaths');

title(countries{cid});

set(gca, 'FontSize', 18);

set(gcf,'position',[10,10,1200,450]);

end